RNA-seq of the roots of Arabidopsis thaliana plants growing in soil treated under different fertilization regimes.
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE129394 | GEO | 2019/04/06
REPOSITORIES: GEO
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Project description:RNA-seq of the roots of Arabidopsis thaliana plants growing in soil treated under different fertilization regimes.
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Project description:Manure amendment to improve soil organic carbon (SOC) content is an important strategy to sustain ecosystem health and crop production. Here, we utilize an 8-year field experiment to evaluate the impacts of organic and chemical fertilizers on SOC and its labile fractions as well as soil microbial and nematode communities in different soil depths of jackfruit (Artocarpus heterophyllus Lam.). Three treatments were designed in this study, including control with no amendment (CK), organic manure (OM), and chemical fertilizer (CF). Results showed that OM significantly increased the abundance of total nematodes, bacterivores, bacteria, and fungi as well as the value of nematode channel ratio (NCR) and maturity index (MI), but decreased plant-parasites and Shannon diversity (H'). Soil microbial and nematode communities in three soil depths were significantly altered by fertilizer application. Acidobacteria and Chloroflexi dominated the bacterial communities of OM soil, while Nitrospira was more prevalent in CF treatment. Organic manure application stimulated some functional groups of the bacterial community related to the C cycle and saprotroph-symbiotroph fungi, while some groups related to the nitrogen cycle, pathotroph-saprotroph-symbiotroph and pathotroph-saprotroph fungi were predominated in CF treatment. Furthermore, OM enhanced the soil pH, contents of total soil N, P, K, and SOC components, as well as jackfruit yield. Chemical fertilizers significantly affected available N, P, and K contents. The results of network analyses show that more significant co-occurrence relationships between SOC components and nematode feeding groups were found in CK and CF treatments. In contrast, SOC components were more related to microbial communities than to nematode in OM soils. Partial least-squares-path modeling (PLS-PM) revealed that fertilization had significant effects on jackfruit yield, which was composed of positive direct (73.6%) and indirect effects (fertilization → fungal community → yield). It was found that the long-term manure application strategy improves soil quality by increasing SOM, pH, and nutrient contents, and the increased microbivorous nematodes abundance enhanced the grazing pressure on microorganisms and concurrently promoted microbial-derived SOC turnover.
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Project description:Shifts in soil bacterial diversity and community composition are suggested to be induced by elevated input of nitrogen (N) fertilization with implications for soil quality, and consequently production. In this study, we evaluated the impacts of recommended fertilization (RF) and conventional fertilization (CF) on soil chemical properties, crop yield, bacterial diversity, and community composition from two long-term experiments conducted in fluvo-aquic soil and black soil of China. Each site comprised of four treatments, i.e., RF N-, RF N+, CF N-, CF N+. No N fertilization was indicated by N- and N fertilization was indicated by N+. Across both sites, N fertilization significantly increased crop yield compared with no N fertilization and RF successfully enhanced crop yield over CF. Interestingly, the RF maintained bacterial diversity, while CF depressed bacterial diversity in the two soils. Microbial taxa performing important ecological roles such as order Rhodospirillales and Bacillales were significantly enhanced in the RF approach, while Rhizobiales declined under CF. Furthermore, the results of partial least square path modeling revealed that soil available phosphorus (AP) negatively affected bacterial diversity while it positively affected bacterial community structure in fluvo-aquic soils. In contrast, soil pH was positively linked with both bacterial diversity and community structure in black soil. Overall, our study demonstrated that RF is an environmentally friendly approach which not only maintained above ground plant productivity, but also preserved belowground microbial populations and important soil variables regulating bacterial communities varied in different soil types.
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Project description:Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen-fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.
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Project description:The data presented in this article are related to the research paper entitled "Changes in N supply pathways under different long-term fertilization regimes in Northeast China" [1]. Seasonal dynamics of soil NH4 +-N, NO3 --N, soil microbial biomass nitrogen (N) and fixed NH4 + were provided on the basis of a 26-year long-term experiment, including six treatments: no fertilizer (CK), recycled manure (M), N and P fertilizers (NP), P and K fertilizers (PK), N, P and K fertilizers (NPK), and NPK fertilizers with recycled manure (NPKM). The presentation of potential N retention and supply through soil microbial biomass N and fixed NH4 + pools at different growth stages is helpful for comparing the effects of different N pools on soil N transformation and assessing synchronies between crop N demand and soil N supply through different N pools.
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